Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2.
Identifieur interne : 000516 ( PubMed/Checkpoint ); précédent : 000515; suivant : 000517Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2.
Auteurs : Xingguang Li [République populaire de Chine] ; Junjie Zai [République populaire de Chine] ; Qiang Zhao [République populaire de Chine] ; Qing Nie [République populaire de Chine] ; Yi Li [République populaire de Chine] ; Brian T. Foley [États-Unis] ; Antoine Chaillon [États-Unis]Source :
- Journal of medical virology [ 1096-9071 ] ; 2020.
Abstract
To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10-3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.
DOI: 10.1002/jmv.25731
PubMed: 32104911
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Foley</name><affiliation wicri:level="2"><nlm:affiliation>HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Nouveau-Mexique</region></placeName><wicri:cityArea>HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos</wicri:cityArea></affiliation></author><author><name sortKey="Chaillon, Antoine" sort="Chaillon, Antoine" uniqKey="Chaillon A" first="Antoine" last="Chaillon">Antoine Chaillon</name><affiliation wicri:level="2"><nlm:affiliation>Department of Medicine, University of California San Diego, La Jolla, California.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Medicine, University of California San Diego, La Jolla</wicri:cityArea></affiliation></author></analytic><series><title level="j">Journal of medical virology</title><idno type="eISSN">1096-9071</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10<sup>-3</sup> substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32104911</PMID><DateRevised><Year>2020</Year><Month>03</Month><Day>11</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-9071</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Feb</Month><Day>27</Day></PubDate></JournalIssue><Title>Journal of medical virology</Title><ISOAbbreviation>J. Med. Virol.</ISOAbbreviation></Journal><ArticleTitle>Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1002/jmv.25731</ELocationID><Abstract><AbstractText>To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10<sup>-3</sup> substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.</AbstractText><CopyrightInformation>© 2020 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Xingguang</ForeName><Initials>X</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-3470-2196</Identifier><AffiliationInfo><Affiliation>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zai</LastName><ForeName>Junjie</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Qiang</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Precision Cancer Center Airport Center, Tianjin Cancer Hospital Airport Hospital, Tianjin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nie</LastName><ForeName>Qing</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Foley</LastName><ForeName>Brian T</ForeName><Initials>BT</Initials><AffiliationInfo><Affiliation>HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chaillon</LastName><ForeName>Antoine</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Medicine, University of California San Diego, La Jolla, California.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><Agency>K.C. Wong Magna Fund in Ningbo University</Agency><Country></Country></Grant><Grant><GrantID>31470268</GrantID><Agency>National Natural Science Foundation of China</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Med Virol</MedlineTA><NlmUniqueID>7705876</NlmUniqueID><ISSNLinking>0146-6615</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword><Keyword MajorTopicYN="N">TMRCA</Keyword><Keyword MajorTopicYN="N">cross-species transmission</Keyword><Keyword MajorTopicYN="N">evolutionary rate</Keyword><Keyword MajorTopicYN="N">potential intermediate animal host</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>02</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32104911</ArticleId><ArticleId IdType="doi">10.1002/jmv.25731</ArticleId></ArticleIdList><ReferenceList><Title>REFERENCES</Title><Reference><Citation>Chan JFW, Yuan S, Kok KH, et al. 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Foley</name></region><name sortKey="Chaillon, Antoine" sort="Chaillon, Antoine" uniqKey="Chaillon A" first="Antoine" last="Chaillon">Antoine Chaillon</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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